Multiple sequence alignment - TraesCS3D01G276300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3D01G276300 chr3D 100.000 3469 0 0 1 3469 383173761 383170293 0.000000e+00 6407
1 TraesCS3D01G276300 chr3D 89.286 1764 145 31 695 2441 149758703 149760439 0.000000e+00 2170
2 TraesCS3D01G276300 chr3D 92.205 821 57 4 2649 3469 336050 336863 0.000000e+00 1155
3 TraesCS3D01G276300 chr3D 97.738 619 13 1 1 619 383180723 383180106 0.000000e+00 1064
4 TraesCS3D01G276300 chr7D 93.321 2785 161 11 693 3469 503838184 503835417 0.000000e+00 4089
5 TraesCS3D01G276300 chr7D 94.618 799 36 2 1825 2623 519747677 519748468 0.000000e+00 1230
6 TraesCS3D01G276300 chr7D 92.665 818 53 3 2652 3469 531065818 531065008 0.000000e+00 1171
7 TraesCS3D01G276300 chr7D 97.092 619 16 2 1 619 93073253 93072637 0.000000e+00 1042
8 TraesCS3D01G276300 chr4D 94.433 2425 118 11 695 3111 470184638 470182223 0.000000e+00 3714
9 TraesCS3D01G276300 chr4D 92.326 821 56 4 2649 3469 491383407 491384220 0.000000e+00 1160
10 TraesCS3D01G276300 chr7B 89.802 2775 221 28 694 3463 43570136 43572853 0.000000e+00 3500
11 TraesCS3D01G276300 chr7B 90.406 2439 199 26 695 3121 730310146 730312561 0.000000e+00 3175
12 TraesCS3D01G276300 chr7B 89.363 1946 169 24 695 2621 672859561 672857635 0.000000e+00 2412
13 TraesCS3D01G276300 chr7B 91.897 1703 125 9 1768 3469 156407289 156405599 0.000000e+00 2368
14 TraesCS3D01G276300 chr7B 91.905 803 57 3 2169 2971 610669818 610669024 0.000000e+00 1116
15 TraesCS3D01G276300 chr7B 85.220 318 41 4 695 1011 672845630 672845942 4.320000e-84 322
16 TraesCS3D01G276300 chr1A 94.263 2179 101 13 695 2869 518113446 518115604 0.000000e+00 3310
17 TraesCS3D01G276300 chr6D 89.207 1955 139 34 695 2621 25731321 25733231 0.000000e+00 2375
18 TraesCS3D01G276300 chr6D 92.579 822 53 4 2649 3469 25733228 25734042 0.000000e+00 1173
19 TraesCS3D01G276300 chr6D 97.078 616 16 2 1 616 31283474 31284087 0.000000e+00 1037
20 TraesCS3D01G276300 chr6D 97.078 616 17 1 1 616 97457098 97457712 0.000000e+00 1037
21 TraesCS3D01G276300 chr5A 87.344 1762 165 41 694 2441 396679716 396677999 0.000000e+00 1965
22 TraesCS3D01G276300 chr2D 92.326 821 56 3 2649 3469 617342661 617343474 0.000000e+00 1160
23 TraesCS3D01G276300 chr2D 97.078 616 17 1 1 616 43048620 43049234 0.000000e+00 1037
24 TraesCS3D01G276300 chr5D 97.092 619 17 1 1 619 480903379 480902762 0.000000e+00 1042
25 TraesCS3D01G276300 chr5D 96.774 620 18 2 1 619 300169078 300168460 0.000000e+00 1033
26 TraesCS3D01G276300 chr1D 96.931 619 17 2 1 619 334306079 334305463 0.000000e+00 1037
27 TraesCS3D01G276300 chr1D 96.921 617 17 2 1 616 312892680 312893295 0.000000e+00 1033
28 TraesCS3D01G276300 chr6B 85.173 607 68 18 695 1289 142984893 142984297 1.380000e-168 603


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G276300 chr3D 383170293 383173761 3468 True 6407 6407 100.000 1 3469 1 chr3D.!!$R1 3468
1 TraesCS3D01G276300 chr3D 149758703 149760439 1736 False 2170 2170 89.286 695 2441 1 chr3D.!!$F2 1746
2 TraesCS3D01G276300 chr3D 336050 336863 813 False 1155 1155 92.205 2649 3469 1 chr3D.!!$F1 820
3 TraesCS3D01G276300 chr3D 383180106 383180723 617 True 1064 1064 97.738 1 619 1 chr3D.!!$R2 618
4 TraesCS3D01G276300 chr7D 503835417 503838184 2767 True 4089 4089 93.321 693 3469 1 chr7D.!!$R2 2776
5 TraesCS3D01G276300 chr7D 519747677 519748468 791 False 1230 1230 94.618 1825 2623 1 chr7D.!!$F1 798
6 TraesCS3D01G276300 chr7D 531065008 531065818 810 True 1171 1171 92.665 2652 3469 1 chr7D.!!$R3 817
7 TraesCS3D01G276300 chr7D 93072637 93073253 616 True 1042 1042 97.092 1 619 1 chr7D.!!$R1 618
8 TraesCS3D01G276300 chr4D 470182223 470184638 2415 True 3714 3714 94.433 695 3111 1 chr4D.!!$R1 2416
9 TraesCS3D01G276300 chr4D 491383407 491384220 813 False 1160 1160 92.326 2649 3469 1 chr4D.!!$F1 820
10 TraesCS3D01G276300 chr7B 43570136 43572853 2717 False 3500 3500 89.802 694 3463 1 chr7B.!!$F1 2769
11 TraesCS3D01G276300 chr7B 730310146 730312561 2415 False 3175 3175 90.406 695 3121 1 chr7B.!!$F3 2426
12 TraesCS3D01G276300 chr7B 672857635 672859561 1926 True 2412 2412 89.363 695 2621 1 chr7B.!!$R3 1926
13 TraesCS3D01G276300 chr7B 156405599 156407289 1690 True 2368 2368 91.897 1768 3469 1 chr7B.!!$R1 1701
14 TraesCS3D01G276300 chr7B 610669024 610669818 794 True 1116 1116 91.905 2169 2971 1 chr7B.!!$R2 802
15 TraesCS3D01G276300 chr1A 518113446 518115604 2158 False 3310 3310 94.263 695 2869 1 chr1A.!!$F1 2174
16 TraesCS3D01G276300 chr6D 25731321 25734042 2721 False 1774 2375 90.893 695 3469 2 chr6D.!!$F3 2774
17 TraesCS3D01G276300 chr6D 31283474 31284087 613 False 1037 1037 97.078 1 616 1 chr6D.!!$F1 615
18 TraesCS3D01G276300 chr6D 97457098 97457712 614 False 1037 1037 97.078 1 616 1 chr6D.!!$F2 615
19 TraesCS3D01G276300 chr5A 396677999 396679716 1717 True 1965 1965 87.344 694 2441 1 chr5A.!!$R1 1747
20 TraesCS3D01G276300 chr2D 617342661 617343474 813 False 1160 1160 92.326 2649 3469 1 chr2D.!!$F2 820
21 TraesCS3D01G276300 chr2D 43048620 43049234 614 False 1037 1037 97.078 1 616 1 chr2D.!!$F1 615
22 TraesCS3D01G276300 chr5D 480902762 480903379 617 True 1042 1042 97.092 1 619 1 chr5D.!!$R2 618
23 TraesCS3D01G276300 chr5D 300168460 300169078 618 True 1033 1033 96.774 1 619 1 chr5D.!!$R1 618
24 TraesCS3D01G276300 chr1D 334305463 334306079 616 True 1037 1037 96.931 1 619 1 chr1D.!!$R1 618
25 TraesCS3D01G276300 chr1D 312892680 312893295 615 False 1033 1033 96.921 1 616 1 chr1D.!!$F1 615
26 TraesCS3D01G276300 chr6B 142984297 142984893 596 True 603 603 85.173 695 1289 1 chr6B.!!$R1 594

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
624 627 0.034380 TCAGTACTCCCTCTGTCCCG 60.034 60.0 0.00 0.0 33.89 5.14 F
662 665 0.175073 GACACGGCGGAGGAGTAATT 59.825 55.0 13.24 0.0 0.00 1.40 F
1426 1449 0.546122 TTGAAGGCACTGACACTGGT 59.454 50.0 0.00 0.0 40.86 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2212 2276 0.251354 TCAGGAGCTCAGCAATGACC 59.749 55.0 17.19 0.00 0.00 4.02 R
2346 2414 0.264359 AGGCTGATCAGTCCTAGGCT 59.736 55.0 27.23 16.08 40.68 4.58 R
3359 3444 0.534652 TGGGTTGCCATGCTTTTTGC 60.535 50.0 0.00 0.00 43.25 3.68 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 2.270352 TTCCGTAATGCATCATCCCC 57.730 50.000 0.00 0.00 0.00 4.81
186 187 2.092592 TCGGAGACACCTGTAGAGCATA 60.093 50.000 0.00 0.00 36.31 3.14
214 215 1.758280 TCACCCAGTTACGTTGTGACT 59.242 47.619 0.00 0.00 32.61 3.41
247 248 5.299279 CACACAAAGTGTTCCTCTGGTATTT 59.701 40.000 0.00 0.00 45.08 1.40
526 528 8.943002 ACTAAGTTTCCGGTTAATACAATTCTG 58.057 33.333 0.00 0.00 0.00 3.02
616 619 4.103311 GGCATATTTCCTTCAGTACTCCCT 59.897 45.833 0.00 0.00 0.00 4.20
617 620 5.301555 GCATATTTCCTTCAGTACTCCCTC 58.698 45.833 0.00 0.00 0.00 4.30
618 621 5.071115 GCATATTTCCTTCAGTACTCCCTCT 59.929 44.000 0.00 0.00 0.00 3.69
619 622 6.520272 CATATTTCCTTCAGTACTCCCTCTG 58.480 44.000 0.00 0.00 0.00 3.35
620 623 3.544698 TTCCTTCAGTACTCCCTCTGT 57.455 47.619 0.00 0.00 33.89 3.41
621 624 3.088789 TCCTTCAGTACTCCCTCTGTC 57.911 52.381 0.00 0.00 33.89 3.51
622 625 2.104170 CCTTCAGTACTCCCTCTGTCC 58.896 57.143 0.00 0.00 33.89 4.02
623 626 2.104170 CTTCAGTACTCCCTCTGTCCC 58.896 57.143 0.00 0.00 33.89 4.46
624 627 0.034380 TCAGTACTCCCTCTGTCCCG 60.034 60.000 0.00 0.00 33.89 5.14
625 628 0.323542 CAGTACTCCCTCTGTCCCGT 60.324 60.000 0.00 0.00 0.00 5.28
626 629 1.064906 CAGTACTCCCTCTGTCCCGTA 60.065 57.143 0.00 0.00 0.00 4.02
627 630 1.637553 AGTACTCCCTCTGTCCCGTAA 59.362 52.381 0.00 0.00 0.00 3.18
628 631 2.244252 AGTACTCCCTCTGTCCCGTAAT 59.756 50.000 0.00 0.00 0.00 1.89
629 632 3.461085 AGTACTCCCTCTGTCCCGTAATA 59.539 47.826 0.00 0.00 0.00 0.98
630 633 3.614568 ACTCCCTCTGTCCCGTAATAT 57.385 47.619 0.00 0.00 0.00 1.28
631 634 4.736611 ACTCCCTCTGTCCCGTAATATA 57.263 45.455 0.00 0.00 0.00 0.86
632 635 5.070823 ACTCCCTCTGTCCCGTAATATAA 57.929 43.478 0.00 0.00 0.00 0.98
633 636 5.461327 ACTCCCTCTGTCCCGTAATATAAA 58.539 41.667 0.00 0.00 0.00 1.40
634 637 6.082707 ACTCCCTCTGTCCCGTAATATAAAT 58.917 40.000 0.00 0.00 0.00 1.40
635 638 7.243824 ACTCCCTCTGTCCCGTAATATAAATA 58.756 38.462 0.00 0.00 0.00 1.40
636 639 7.899709 ACTCCCTCTGTCCCGTAATATAAATAT 59.100 37.037 0.00 0.00 0.00 1.28
637 640 9.417561 CTCCCTCTGTCCCGTAATATAAATATA 57.582 37.037 0.00 0.00 0.00 0.86
638 641 9.947189 TCCCTCTGTCCCGTAATATAAATATAT 57.053 33.333 0.00 0.00 0.00 0.86
652 655 9.834628 AATATAAATATATTTTTGACACGGCGG 57.165 29.630 15.64 2.35 35.86 6.13
653 656 5.821516 AAATATATTTTTGACACGGCGGA 57.178 34.783 13.24 0.00 0.00 5.54
654 657 5.418310 AATATATTTTTGACACGGCGGAG 57.582 39.130 13.24 5.87 0.00 4.63
655 658 1.444836 TATTTTTGACACGGCGGAGG 58.555 50.000 13.24 2.44 0.00 4.30
656 659 0.250553 ATTTTTGACACGGCGGAGGA 60.251 50.000 13.24 0.00 0.00 3.71
657 660 0.882927 TTTTTGACACGGCGGAGGAG 60.883 55.000 13.24 0.00 0.00 3.69
658 661 2.035237 TTTTGACACGGCGGAGGAGT 62.035 55.000 13.24 0.91 0.00 3.85
659 662 1.180456 TTTGACACGGCGGAGGAGTA 61.180 55.000 13.24 0.00 0.00 2.59
660 663 1.180456 TTGACACGGCGGAGGAGTAA 61.180 55.000 13.24 0.00 0.00 2.24
661 664 0.968901 TGACACGGCGGAGGAGTAAT 60.969 55.000 13.24 0.00 0.00 1.89
662 665 0.175073 GACACGGCGGAGGAGTAATT 59.825 55.000 13.24 0.00 0.00 1.40
663 666 1.406539 GACACGGCGGAGGAGTAATTA 59.593 52.381 13.24 0.00 0.00 1.40
664 667 1.407979 ACACGGCGGAGGAGTAATTAG 59.592 52.381 13.24 0.00 0.00 1.73
665 668 1.407979 CACGGCGGAGGAGTAATTAGT 59.592 52.381 13.24 0.00 0.00 2.24
666 669 2.620115 CACGGCGGAGGAGTAATTAGTA 59.380 50.000 13.24 0.00 0.00 1.82
667 670 2.620585 ACGGCGGAGGAGTAATTAGTAC 59.379 50.000 13.24 0.00 0.00 2.73
668 671 2.350197 CGGCGGAGGAGTAATTAGTACG 60.350 54.545 0.00 0.56 37.81 3.67
669 672 2.620585 GGCGGAGGAGTAATTAGTACGT 59.379 50.000 0.00 0.00 37.81 3.57
670 673 3.815401 GGCGGAGGAGTAATTAGTACGTA 59.185 47.826 0.00 0.00 37.81 3.57
671 674 4.083590 GGCGGAGGAGTAATTAGTACGTAG 60.084 50.000 0.00 0.00 37.81 3.51
672 675 4.083590 GCGGAGGAGTAATTAGTACGTAGG 60.084 50.000 0.00 0.00 37.81 3.18
673 676 4.083590 CGGAGGAGTAATTAGTACGTAGGC 60.084 50.000 0.00 0.00 37.81 3.93
674 677 4.083590 GGAGGAGTAATTAGTACGTAGGCG 60.084 50.000 0.00 0.00 44.93 5.52
707 711 2.494059 CTGTCCCGAGTGTTTGACAAT 58.506 47.619 0.00 0.00 37.29 2.71
739 744 4.404098 GGGGTTCGCGTCCCACAT 62.404 66.667 30.86 0.00 46.26 3.21
918 924 1.495509 GCGCATGTGCTGTCGTTAA 59.504 52.632 23.77 0.00 39.32 2.01
991 998 2.997315 CTCGTCCCCACCAGCTCA 60.997 66.667 0.00 0.00 0.00 4.26
1014 1021 1.684049 CTCTCCCCCGAGCTCACTT 60.684 63.158 15.40 0.00 35.94 3.16
1025 1032 1.132262 GAGCTCACTTCACTCCTCTCG 59.868 57.143 9.40 0.00 0.00 4.04
1031 1038 1.181786 CTTCACTCCTCTCGGCTCTT 58.818 55.000 0.00 0.00 0.00 2.85
1426 1449 0.546122 TTGAAGGCACTGACACTGGT 59.454 50.000 0.00 0.00 40.86 4.00
1433 1456 1.203523 GCACTGACACTGGTAGGAGAG 59.796 57.143 0.00 0.00 0.00 3.20
1445 1468 5.144100 CTGGTAGGAGAGTCATAGGATGTT 58.856 45.833 0.00 0.00 0.00 2.71
1451 1474 7.395525 AGGAGAGTCATAGGATGTTCTACTA 57.604 40.000 0.00 0.00 35.78 1.82
1616 1652 8.655092 GCATAGAGCACTAGAAACATATTGATC 58.345 37.037 0.00 0.00 44.79 2.92
1725 1780 7.718272 TGTTAACTATGGTGTTCACTGTAAC 57.282 36.000 7.22 0.00 0.00 2.50
1763 1822 2.030007 GGATGGTGTGAATTGTGGTGTG 60.030 50.000 0.00 0.00 0.00 3.82
1967 2030 7.950512 TGATGTGTCCAAGTTGTTTGATTATT 58.049 30.769 1.45 0.00 39.21 1.40
1974 2037 8.739972 GTCCAAGTTGTTTGATTATTAGGATGT 58.260 33.333 1.45 0.00 39.21 3.06
2042 2105 4.640364 ACTGAAGGAGAAGAAGAAGCAAG 58.360 43.478 0.00 0.00 0.00 4.01
2212 2276 4.806640 AGAGAAGAAGAAGCTGGAGAAG 57.193 45.455 0.00 0.00 0.00 2.85
2277 2341 1.742268 GCTGGACAAGATCAAGGAAGC 59.258 52.381 0.00 0.00 0.00 3.86
2278 2342 2.363683 CTGGACAAGATCAAGGAAGCC 58.636 52.381 0.00 0.00 0.00 4.35
2647 2718 9.994432 CTGCAAGAAAGGTAAACAATATCTAAG 57.006 33.333 0.00 0.00 34.07 2.18
2656 2727 9.515226 AGGTAAACAATATCTAAGCAAGTTCAA 57.485 29.630 0.00 0.00 0.00 2.69
2811 2882 5.211174 ACACCCTACTAAACTGACAGAAC 57.789 43.478 10.08 0.00 0.00 3.01
2869 2954 6.755141 GGCGATAACTGTTGTAACTGAATCTA 59.245 38.462 2.69 0.00 0.00 1.98
2924 3009 1.878522 GCTATGCGACCTGACCGTG 60.879 63.158 0.00 0.00 0.00 4.94
3014 3099 0.760945 GATGGGAGGAGGATGTCGGT 60.761 60.000 0.00 0.00 0.00 4.69
3022 3107 1.608717 GAGGATGTCGGTGAGCCAGT 61.609 60.000 0.00 0.00 34.09 4.00
3046 3131 1.976132 CTGGTGGGGCGATGATCTGT 61.976 60.000 0.00 0.00 0.00 3.41
3116 3201 0.485543 TGGAGGGATATAGCGGTGGA 59.514 55.000 0.00 0.00 0.00 4.02
3196 3281 0.520404 GCATGTCGATGGGCATGATC 59.480 55.000 24.37 5.43 43.60 2.92
3204 3289 1.425066 GATGGGCATGATCCCCTTACA 59.575 52.381 8.20 0.00 45.97 2.41
3243 3328 1.144716 CCATGCGCTGCTTCTCCTA 59.855 57.895 9.73 0.00 0.00 2.94
3296 3381 1.340399 ATCCATGAGCCCTTCTGCGA 61.340 55.000 0.00 0.00 36.02 5.10
3318 3403 5.107182 CGATGTTGTATCTCATGGCAATCTC 60.107 44.000 0.00 0.00 0.00 2.75
3331 3416 2.092968 GGCAATCTCCATGTAGTCCACA 60.093 50.000 0.00 0.00 42.69 4.17
3414 3501 1.739608 AAGGGGTTCAGCCATGGGTT 61.740 55.000 15.37 0.00 39.65 4.11
3459 3546 3.388024 GCCATGGATGTAGGTAGAGTGAA 59.612 47.826 18.40 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 1.830408 CTCTGGGCCCTCTCGGTAG 60.830 68.421 25.70 10.33 0.00 3.18
186 187 7.825270 TCACAACGTAACTGGGTGATTATAAAT 59.175 33.333 0.00 0.00 33.88 1.40
214 215 5.359576 AGGAACACTTTGTGTGCTATCAAAA 59.640 36.000 8.51 0.00 46.79 2.44
247 248 5.366477 TGACTATGAGATTATGCAACTCCCA 59.634 40.000 0.00 0.00 0.00 4.37
626 629 9.834628 CCGCCGTGTCAAAAATATATTTATATT 57.165 29.630 11.07 0.00 39.79 1.28
627 630 9.221933 TCCGCCGTGTCAAAAATATATTTATAT 57.778 29.630 11.07 0.00 0.00 0.86
628 631 8.604640 TCCGCCGTGTCAAAAATATATTTATA 57.395 30.769 11.07 0.00 0.00 0.98
629 632 7.308348 CCTCCGCCGTGTCAAAAATATATTTAT 60.308 37.037 11.07 0.01 0.00 1.40
630 633 6.017770 CCTCCGCCGTGTCAAAAATATATTTA 60.018 38.462 11.07 0.00 0.00 1.40
631 634 5.220970 CCTCCGCCGTGTCAAAAATATATTT 60.221 40.000 4.81 4.81 0.00 1.40
632 635 4.274950 CCTCCGCCGTGTCAAAAATATATT 59.725 41.667 0.00 0.00 0.00 1.28
633 636 3.813166 CCTCCGCCGTGTCAAAAATATAT 59.187 43.478 0.00 0.00 0.00 0.86
634 637 3.118702 TCCTCCGCCGTGTCAAAAATATA 60.119 43.478 0.00 0.00 0.00 0.86
635 638 2.014128 CCTCCGCCGTGTCAAAAATAT 58.986 47.619 0.00 0.00 0.00 1.28
636 639 1.002201 TCCTCCGCCGTGTCAAAAATA 59.998 47.619 0.00 0.00 0.00 1.40
637 640 0.250553 TCCTCCGCCGTGTCAAAAAT 60.251 50.000 0.00 0.00 0.00 1.82
638 641 0.882927 CTCCTCCGCCGTGTCAAAAA 60.883 55.000 0.00 0.00 0.00 1.94
639 642 1.301401 CTCCTCCGCCGTGTCAAAA 60.301 57.895 0.00 0.00 0.00 2.44
640 643 1.180456 TACTCCTCCGCCGTGTCAAA 61.180 55.000 0.00 0.00 0.00 2.69
641 644 1.180456 TTACTCCTCCGCCGTGTCAA 61.180 55.000 0.00 0.00 0.00 3.18
642 645 0.968901 ATTACTCCTCCGCCGTGTCA 60.969 55.000 0.00 0.00 0.00 3.58
643 646 0.175073 AATTACTCCTCCGCCGTGTC 59.825 55.000 0.00 0.00 0.00 3.67
644 647 1.407979 CTAATTACTCCTCCGCCGTGT 59.592 52.381 0.00 0.00 0.00 4.49
645 648 1.407979 ACTAATTACTCCTCCGCCGTG 59.592 52.381 0.00 0.00 0.00 4.94
646 649 1.772836 ACTAATTACTCCTCCGCCGT 58.227 50.000 0.00 0.00 0.00 5.68
647 650 2.350197 CGTACTAATTACTCCTCCGCCG 60.350 54.545 0.00 0.00 0.00 6.46
648 651 2.620585 ACGTACTAATTACTCCTCCGCC 59.379 50.000 0.00 0.00 0.00 6.13
649 652 3.978718 ACGTACTAATTACTCCTCCGC 57.021 47.619 0.00 0.00 0.00 5.54
650 653 4.083590 GCCTACGTACTAATTACTCCTCCG 60.084 50.000 0.00 0.00 0.00 4.63
651 654 4.083590 CGCCTACGTACTAATTACTCCTCC 60.084 50.000 0.00 0.00 33.53 4.30
652 655 5.028428 CGCCTACGTACTAATTACTCCTC 57.972 47.826 0.00 0.00 33.53 3.71
667 670 1.335689 GGGAGTAATGCTACGCCTACG 60.336 57.143 5.98 0.00 44.91 3.51
668 671 1.962100 AGGGAGTAATGCTACGCCTAC 59.038 52.381 5.98 0.00 44.91 3.18
669 672 1.961394 CAGGGAGTAATGCTACGCCTA 59.039 52.381 5.98 0.00 44.91 3.93
670 673 0.753262 CAGGGAGTAATGCTACGCCT 59.247 55.000 5.98 0.00 44.91 5.52
671 674 0.464452 ACAGGGAGTAATGCTACGCC 59.536 55.000 0.00 0.00 44.84 5.68
672 675 1.538419 GGACAGGGAGTAATGCTACGC 60.538 57.143 0.00 0.00 32.87 4.42
673 676 1.068741 GGGACAGGGAGTAATGCTACG 59.931 57.143 0.00 0.00 32.87 3.51
674 677 1.068741 CGGGACAGGGAGTAATGCTAC 59.931 57.143 0.00 0.00 0.00 3.58
675 678 1.063492 TCGGGACAGGGAGTAATGCTA 60.063 52.381 0.00 0.00 0.00 3.49
676 679 0.325296 TCGGGACAGGGAGTAATGCT 60.325 55.000 0.00 0.00 0.00 3.79
677 680 0.105039 CTCGGGACAGGGAGTAATGC 59.895 60.000 0.00 0.00 0.00 3.56
678 681 1.137086 CACTCGGGACAGGGAGTAATG 59.863 57.143 0.00 0.00 41.37 1.90
679 682 1.273098 ACACTCGGGACAGGGAGTAAT 60.273 52.381 0.00 0.00 41.37 1.89
680 683 0.113776 ACACTCGGGACAGGGAGTAA 59.886 55.000 0.00 0.00 41.37 2.24
681 684 0.113776 AACACTCGGGACAGGGAGTA 59.886 55.000 0.00 0.00 41.37 2.59
682 685 0.763223 AAACACTCGGGACAGGGAGT 60.763 55.000 0.00 0.00 43.99 3.85
683 686 0.320771 CAAACACTCGGGACAGGGAG 60.321 60.000 0.00 0.00 36.36 4.30
684 687 0.761323 TCAAACACTCGGGACAGGGA 60.761 55.000 0.00 0.00 0.00 4.20
685 688 0.602905 GTCAAACACTCGGGACAGGG 60.603 60.000 0.00 0.00 0.00 4.45
686 689 0.105964 TGTCAAACACTCGGGACAGG 59.894 55.000 0.00 0.00 35.51 4.00
687 690 1.948104 TTGTCAAACACTCGGGACAG 58.052 50.000 0.00 0.00 40.90 3.51
688 691 2.631160 ATTGTCAAACACTCGGGACA 57.369 45.000 0.00 0.00 38.41 4.02
689 692 4.514066 AGTTTATTGTCAAACACTCGGGAC 59.486 41.667 0.00 0.00 40.22 4.46
690 693 4.710324 AGTTTATTGTCAAACACTCGGGA 58.290 39.130 0.00 0.00 40.22 5.14
691 694 5.106830 GGTAGTTTATTGTCAAACACTCGGG 60.107 44.000 1.99 0.00 40.22 5.14
707 711 4.563374 GCGAACCCCTAAAGTGGTAGTTTA 60.563 45.833 0.00 0.00 33.52 2.01
904 910 0.796312 CGGCTTTAACGACAGCACAT 59.204 50.000 0.00 0.00 37.81 3.21
905 911 1.837538 GCGGCTTTAACGACAGCACA 61.838 55.000 0.00 0.00 37.81 4.57
991 998 2.363147 GCTCGGGGGAGAGTGAGT 60.363 66.667 0.00 0.00 40.26 3.41
1025 1032 2.470983 AACAGAAGCAGAGAAGAGCC 57.529 50.000 0.00 0.00 0.00 4.70
1031 1038 5.537188 GAGAAGAAGAAACAGAAGCAGAGA 58.463 41.667 0.00 0.00 0.00 3.10
1085 1092 2.031919 TCGTTGCTGTTCGGCCAT 59.968 55.556 2.24 0.00 0.00 4.40
1393 1416 3.386078 TGCCTTCAAATGCCACAAACTTA 59.614 39.130 0.00 0.00 0.00 2.24
1426 1449 7.395525 AGTAGAACATCCTATGACTCTCCTA 57.604 40.000 0.00 0.00 31.69 2.94
1433 1456 9.915629 CATTACCTTAGTAGAACATCCTATGAC 57.084 37.037 0.00 0.00 0.00 3.06
1687 1737 9.423061 ACCATAGTTAACAAGCAAATTCAATTC 57.577 29.630 8.61 0.00 0.00 2.17
1688 1738 9.206870 CACCATAGTTAACAAGCAAATTCAATT 57.793 29.630 8.61 0.00 0.00 2.32
1689 1739 8.367156 ACACCATAGTTAACAAGCAAATTCAAT 58.633 29.630 8.61 0.00 0.00 2.57
1690 1740 7.721402 ACACCATAGTTAACAAGCAAATTCAA 58.279 30.769 8.61 0.00 0.00 2.69
1691 1741 7.283625 ACACCATAGTTAACAAGCAAATTCA 57.716 32.000 8.61 0.00 0.00 2.57
1725 1780 8.928733 CACACCATCCTGAAAATCAATTTAAAG 58.071 33.333 0.00 0.00 0.00 1.85
1763 1822 2.191641 GGCATCTCCCACTCCAGC 59.808 66.667 0.00 0.00 0.00 4.85
1786 1847 5.242795 AGCACCTTTGTAGAATTACAGGT 57.757 39.130 0.00 0.00 40.68 4.00
1988 2051 1.274167 CTGGCTTGTGCAATCCATGTT 59.726 47.619 7.79 0.00 41.91 2.71
2042 2105 3.062042 CAATTTTTGCCTGCTCCTCAAC 58.938 45.455 0.00 0.00 0.00 3.18
2212 2276 0.251354 TCAGGAGCTCAGCAATGACC 59.749 55.000 17.19 0.00 0.00 4.02
2277 2341 0.898320 ACTTCACTCCTCCATCACGG 59.102 55.000 0.00 0.00 0.00 4.94
2278 2342 1.404717 CCACTTCACTCCTCCATCACG 60.405 57.143 0.00 0.00 0.00 4.35
2341 2409 4.528596 GGCTGATCAGTCCTAGGCTAATTA 59.471 45.833 23.38 0.00 33.44 1.40
2342 2410 3.326297 GGCTGATCAGTCCTAGGCTAATT 59.674 47.826 23.38 0.00 33.44 1.40
2346 2414 0.264359 AGGCTGATCAGTCCTAGGCT 59.736 55.000 27.23 16.08 40.68 4.58
2610 2680 2.502142 TTCTTGCAGCCTGTGATGAT 57.498 45.000 0.00 0.00 0.00 2.45
2647 2718 6.753744 ACTTCTCTGAATTTGTTTGAACTTGC 59.246 34.615 0.00 0.00 0.00 4.01
2656 2727 7.122650 TGTCTTCCAAACTTCTCTGAATTTGTT 59.877 33.333 0.00 0.00 31.48 2.83
2811 2882 8.763049 TGTGAGATTCAGTTATGTCTGTTTAG 57.237 34.615 0.00 0.00 36.85 1.85
2882 2967 2.357154 GGCATGGGACCTAACAATCTGT 60.357 50.000 0.00 0.00 0.00 3.41
2895 2980 2.517414 GCATAGCAGGGCATGGGA 59.483 61.111 0.00 0.00 0.00 4.37
2924 3009 2.805099 CTCAAGTCAAGCAAGAGGTGTC 59.195 50.000 0.00 0.00 0.00 3.67
3022 3107 2.687200 ATCGCCCCACCAGCACTA 60.687 61.111 0.00 0.00 0.00 2.74
3046 3131 1.412710 GGCAATGACGATGAGGACCTA 59.587 52.381 0.00 0.00 0.00 3.08
3116 3201 3.637273 GAGGGAACGGTGGGCAGT 61.637 66.667 0.00 0.00 0.00 4.40
3243 3328 1.902508 TGAGGAAGAAGGCGATGACTT 59.097 47.619 0.00 0.00 31.13 3.01
3296 3381 5.068636 GGAGATTGCCATGAGATACAACAT 58.931 41.667 0.00 0.00 0.00 2.71
3318 3403 5.359194 AGACCTATTTGTGGACTACATGG 57.641 43.478 0.00 0.00 39.48 3.66
3359 3444 0.534652 TGGGTTGCCATGCTTTTTGC 60.535 50.000 0.00 0.00 43.25 3.68
3414 3501 1.137086 GTTCTTCCTCATCTGCGCCTA 59.863 52.381 4.18 0.00 0.00 3.93


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.